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Background Studies have shown an increased prevalence of irritable bowel syndrome (IBS) after acute gastroenteritis. Food as a precipitating and perpetuating factor in IBS has gained recent interest, but food intolerance following gastroenteritis is less investigated. The aims of this study were firstly, to compare perceived food intolerance in a group previously exposed to Giardia lamblia with a control group; secondly, to explore the relation with IBS status; and thirdly, to investigate associations with content of fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) in foods reported. Methods This is a historical cohort study with mailed questionnaire to 1252 Giardia exposed and a control cohort matched by gender and age. Differences between groups were investigated using bivariate and multivariate analyses. Results The questionnaire response rate in the exposed group was 65.3 % (817/1252) and in the control group 31.4 % (1128/3598). The adjusted odds ratio (OR) for perceived food intolerance for the exposed group was 2.00 with 95 % confidence interval (CI): 1.65 to 2.42, as compared with the control group. Perceived intolerance for dairy products was the most frequently reported intolerance, with an adjusted OR for the exposed of 1.95 (95 % CI: 1.51 to 2.51). Perceived intolerance for fatty foods, vegetables, fruit, cereals and alcohol was also significantly higher in the exposed group. The groups did not differ in perceived intolerance to spicy foods, coffee or soda. The association between exposure to Giardia infection and perceived food intolerance differed between the IBS group and the no-IBS group, but IBS was not a significant effect modifier for the association. Perceived intolerance for high FODMAP foods (adjusted OR 1.91) and low FODMAP foods (adjusted OR 1.55) was significantly associated with exposure status. Conclusion Exposure to Giardia infection was associated with perceived food intolerance 3 years after giardiasis. IBS status did not alter the association between exposure status and perceived food intolerance. Perceived intolerance to high FODMAP foods and low FODMAP foods were both statistically significantly associated with exposure to Giardia infection.